User: Rory Stark

gravatar for Rory Stark
Rory Stark2.8k
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CRUK, Cambridge, UK
Last seen:
1 week, 3 days ago
Joined:
6 years, 6 months ago
Email:
r*********@cruk.cam.ac.uk

I am Principal Scientist, Computational Biology at the University of Cambridge, leading the Analysis Team in the Bioinformatics Core at Cancer Research UK's Cambridge Institute.

Posts by Rory Stark

<prev • 484 results • page 1 of 49 • next >
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Answer: A: Diffbind batch effect blocking error
... `block` is not a parameter to `dba.analyze()`. If you want to do a blocking contrast, you need to add it explicitly using `dba.contrast()`. ...
written 12 days ago by Rory Stark2.8k
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Comment: C: diffBind: differentially bound sites are highly different between using EDGER an
... This is consistent with an experiment that induces a large change in binding, all in one direction. The TMM normalization used by `edgeR` assumes a core of relatively unchanged binding and will over-normalize. In this case, you should use `DESeq2` and `bFullLibrarySize = TRUE`. This is actually the ...
written 23 days ago by Rory Stark2.8k
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Answer: A: diffBind: differentially bound sites are highly different between using EDGER an
... When there is a big difference like that, it is usually down to the different normalization methods. With `bFullLibrarySize=TRUE`, the DESeq2 analysis will perform only a basic normalization to library size, while the edgeR analysis will perform a more substantive adjustment. If there is a large ch ...
written 23 days ago by Rory Stark2.8k
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Answer: A: diffbind change conditions dinamically
... You can add contrasts via `dba.contrast()`, and when you call `dba.analyze()`, the new contrasts will be computed without recounting. If you want to clear all the previous contrasts, you can set `myDBA$contrasts=NULL` before calling `dba.contrast()` and/or `dba.analyze()`. ...
written 5 weeks ago by Rory Stark2.8k
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Answer: A: Error in DBA_OLAP_RATE
... Two issues here. In the first example (`mask=broad_gtsf1$masks$Mutant & broad_gtsf1$masks$WT`), there are no peaksets that are *both* Mutant **and** WT: > sum(broad_gtsf1$masks$Mutant & broad_gtsf1$masks$WT) [1] 0 You should use | (or) -- peaks that are *either* Mutant **or** W ...
written 10 weeks ago by Rory Stark2.8k
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Answer: A: DiffBind returns empty consensus peakset
... This is showing that zero sites have been loaded. One unusual thing I see is that your use of `system.file()` to specify the peaks directories. As you are giving full paths to the peaks (starting with `"/home"`), you shouldn't need to use `system.file()` and specify them as being installed with the ...
written 10 weeks ago by Rory Stark2.8k
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Answer: A: Reading peaks from MACS2 with DiffBind
... You can read in *narrowPeak* files by setting the `PeakCaller` to `"narrow"` in the sample sheet. Alternatively, you can read in the *xls* files created by **MACS2** by setting the `PeakCaller` to `"macs"`. -Rory ...
written 11 weeks ago by Rory Stark2.8k
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Answer: A: DiffBind's MA plots for ChIP-seq - how to properly interpret normalization from
... I'm not sure who is saying that you "should expect that the blue density plot is symmetrical around the X axis (when my data is properly normalized)". While this tends to be true for RNA-seq, in ChIP-seq there can be radical shifts in binding levels between conditions (depending on your treatments). ...
written 11 weeks ago by Rory Stark2.8k
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Answer: A: Diffbind affinity based analysis
... It is most certainly possible for the quantitative (affinity) analysis to be unable to identify differentially bound sites, even when there are peaks called only in one condition. There are a number of reasons why this can occur. First, there may be a number of borderline peaks that are above the ...
written 3 months ago by Rory Stark2.8k
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Answer: A: Can I input peak files from Genrich as input reads in DiffBind?
... Yes, this should work with the `.narrowPeak` files. In the sample sheet, the values in the `PeakCaller` column should be set to `"narrow"`. ...
written 4 months ago by Rory Stark2.8k

Latest awards to Rory Stark

Scholar 23 days ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Scholar 7 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: diffbind finding not differential site
Popular Question 7 months ago, created a question with more than 1,000 views. For diffbind
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Differential analysis of multiple samples with different time points
Popular Question 7 months ago, created a question with more than 1,000 views. For DiffBind & Chip-exo
Scholar 7 months ago, created an answer that has been accepted. For A: dba.count binding matrix coordinates
Popular Question 7 months ago, created a question with more than 1,000 views. For DiffBind annotation
Popular Question 7 months ago, created a question with more than 1,000 views. For DiffBind Question
Scholar 7 months ago, created an answer that has been accepted. For A: DiffBind differential binding normalization with different levels of binding
Popular Question 7 months ago, created a question with more than 1,000 views. For Diffbind: Binding Affinity Heatmap
Popular Question 9 months ago, created a question with more than 1,000 views. For diffbind
Scholar 9 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Scholar 10 months ago, created an answer that has been accepted. For A: DiffBind differential binding normalization with different levels of binding
Scholar 10 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Work with GRanges objects in DiffBind
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Differential analysis of multiple samples with different time points
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: diffbind finding not differential site
Scholar 11 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Scholar 15 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Popular Question 2.2 years ago, created a question with more than 1,000 views. For DiffBind Question
Commentator 2.2 years ago, created a comment with at least 3 up-votes. For C: Diffbind - What exactly is a "consensus" peak set?
Scholar 2.2 years ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Scholar 2.2 years ago, created an answer that has been accepted. For A: DiffBind matrix of values
Popular Question 2.2 years ago, created a question with more than 1,000 views. For diffbind

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